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  • picard 1.139 command errors on but added to path on ubuntu 14.04

    I seem to have trouble with calling picard from the command line but other tools work perfectly.

    path:
    Code:
    /home/cmccabe/Desktop/NGS/bedops-2.14.4/bin:/home/cmccabe/Desktop/NGS/samtools-1.2:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/home/cmccabe/Desktop/NGS/bedtools2-25.0/bin:/home/cmccabe/Desktop/NGS/bbmap-35.59:/home/cmccabe/Desktop/NGS/FastQC-0.11.4:/home/cmccabe/Desktop/NGS/picard-tools-1.139
    The code below throws an error as the picard.jar can not be found:
    Code:
    cmccabe@DTV-A5211QLM:~/Desktop/NGS$ java -jar picard.jar SortSam \
    > INPUT=/home/cmccabe/IDP/mapped_unmatched_adapter_removed_quality_trimmed_NA12878-NextSeq-S1_R1_and_R2.sam \
    > OUTPUT=/home/cmccabe/Desktop/NGS/picard-tools-1.139/sorted_mapped_unmatched_adapter_removed_quality_trimmed_NA12878-NextSeq-S1_R1_and_R2.bam \
    > SORT_ORDER=coordinate
    Error: Unable to access jarfile picard.jar
    However, that same command in a slightly different way works perfectly:
    Code:
    cmccabe@DTV-A5211QLM:~/Desktop/NGS$ java -jar /home/cmccabe/Desktop/NGS/picard-tools-1.139/picard.jar SortSam INPUT=/home/cmccabe/IDP/mapped_unmatched_adapter_removed_quality_trimmed_NA12878-NextSeq-S1_R1_and_R2.sam OUTPUT=/home/cmccabe/Desktop/NGS/picard-tools-1.139/sorted_mapped_unmatched_adapter_removed_quality_trimmed_NA12878-NextSeq-S1_R1_and_R2.bam SORT_ORDER=coordinate
    I guess it's just more out of curiosity why only picard seems to act this way on ubuntu 14.04. Thank you .

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